Biogeochemical cycling papers, Page 2 Category

Link:  https://environmentalmicrobiology.community.uaf.edu/wp-content/uploads/sites/763/2018/02/biogeochemical-evolution-of-domestic-WW-in-septic-systems.pdf

Abstract: This paper presents a conceptual model, developed by synthesizing the results of many researchers, which describes the geochemical evolution of domestic wastewater in conventional on-site septic systems as the result of the interactions of a few major constituents. As described by the model, the evolution of wastewater is driven by the microbially catalyzed redox reactions involving organic C and N in wastewater and occurs in as many as three different redox zones. Anaerobic digestion of organic matter and production of CO2, CH4, and NH4+ predominate in the first zone, which consists mainly of the septic tank. In the second zone, gaseous diffusion through the unsaturated sediments of the drain field supplies O2 for aerobic oxidation of organic C and NH4+ and the consequent decrease in wastewater alkalinity. The NO3- formed by NH4+ oxidation in this zone is the primary adverse impact of septic systems at most sites and is generally an unavoidable consequence of the proper functioning of conventional septic systems. If adequate O2 is not available in the drain field, aerobic digestions is incomplete, and the accumulation of organic matter may cause septic system failure. In the third redox zone, NO3- is reduced to N2 by the anaerobic process of denitrification. However, this setting is rarely found below septic systems due to a lack of labile organic C in the natural setting. Consideration of the changing redox and pH conditions in each zone aids our understanding of the fate of other constituents in septic systems.

Justification: While this is an old paper, the concepts haven’t changed much. I think it is a fantastic example of a simple manmade system that takes advantage of the microbes and nutrients but discusses the potential impacts if favorable conditions don’t exist. While it may not be biologically technical with fancy techniques for analyzing microbes, it is an interesting topic.

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Citation:

Raghoebarsing, A.A., Pol, A., Van de Pas-Schoonen, K.T., Smolders, A.J., Ettwig, K.F., Rijpstra, W.I.C., Schouten, S., Damsté, J.S.S., den Camp, H.J.O., Jetten, M.S. and Strous, M., 2006. A microbial consortium couples anaerobic methane oxidation to denitrification.  Nature,  440(7086), p.918.

 

Abstract:

Modern agriculture has accelerated biological methane and nitrogen cycling on a global scale1,2. Freshwater sediments often receive increased downward fluxes of nitrate from agricultural runoff and upward fluxes of methane generated by anaerobic decomposition3 . In theory, prokaryotes should be capable of using nitrate to oxidize methane anaerobically, but such organisms have neither been observed in nature nor isolated in the laboratory4—8. Microbial oxidation of methane is thus believed to proceed only with oxygen or sulphate9,10. Here we show that the direct, anaerobic oxidation of methane coupled to denitrification of nitrate is possible. A microbial consortium, enriched from anoxic sediments, oxidized methane to carbon dioxide coupled to denitrification in the complete absence of oxygen. This consortium consisted of two microorganisms, a bacterium representing a phylum without any cultured species and an archaeon distantly related to marine methanotrophic Archaea. The detection of relatives of these prokaryotes in different freshwater ecosystems worldwide11—14 indicates that the reaction presented here may make a substantial contribution to biological methane and nitrogen cycles.

 

Link:  https://www.nature.com/articles/nature04617.pdf

 

Justification:

Methane and nitrous oxide (N2O) are both meaningful greenhouse gasses and are released by thawing permafrost as is observed in the Arctic  in the past five to ten years. This paper outlines a newly-discovered consortium of microorganisms which feeds on methane and is capable of fully denitrifying nitrate to dinitrogen. If this consortium is as prevalent as the authors suggest, then it may be a critical component of remediation in rivers heavily affected by heavy agricultural runoff and melting permafrost deposits.

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Link:  https://www.nature.com/articles/ncomms13219

Abstract:

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth’s biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.

Citation:

Parks, D.H.,  Rinke, C.,  Chuvochina, M., (…),  Hugenholtz, P.,  Tyson, G.W., “Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life”,  Nature Microbiology 2(11), pp. 1533-1542

 

Reason for selecting this paper:

This paper gives a good insight about the microbial communities living in aquifers and how do they interact with each other. Underground water is an important source of water to humans and this paper discusses about changes in biogeochemical cycles.

 

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Citation:

Urakawa, H., Dettmar, D. L., & Thomas, S. (2017). The uniqueness and biogeochemical cycling of plant root microbial communities in a floating treatment wetland. Ecological Engineering, 108(Part B), 573-580. doi:10.1016/j.ecoleng.2017.06.066

Article: https://www.sciencedirect.com/science/article/pii/S0925857417303944

Abstract:

Floating treatment wetlands (FTWs) are an innovative type of phytoremediation technique being used to reduce the impact of excess nutrient loading. Plants hydroponically grown on FTWs take up nutrients from water through their roots. In general microbial communities in the rhizosphere are important for healthy growth and nutrient uptake by plants. Despite most of previous studies focused on the nutrient removal processes, very little is known about microbial communities associated with FTW plant roots. The purpose of this study was to characterize the microbiomes revolving around the submerged roots of FTW in a manmade stormwater pond and to elucidate the source of FTW plant root microbiomes. The microbial communities collected from the plant roots  Canna flaccida  (golden canna) and  Juncus effusus  (soft rush), biofilms of plant pot (polyethylene) and floating mat foam (closed-cell urethane), and surrounding water were studied using 16S rRNA gene amplicon sequencing. The FTW plant root microbiomes were dominated by Alphaproteobacteria and Cyanobacteria at the class level, and  Anabaena,  Rhizobium  and  Rhodobacter  at the genus level. Microbial communities of the FTW plant roots showed unique compositions resembling most closely the surrounding water samples while being quite different from the biofilm samples, leading the conclusion that the major source of microbial populations was the surrounding water. However, the dominance of  Rhizobium  species was only observed in the two plant roots and not recognized in the surrounding water samples, indicating that the FTW roots may selectively shape root microbiomes. Unexpectedly, quite a few groups of microbes were associated with the sulfur cycle. This finding indicates that the oxic-anoxic gradient is formed in the FTW rhizosphere, and this environmental gradient assists to extend the phylogenetic and functional diversities of microorganisms. We anticipate the presence of intrinsic rhizosphere microbiomes and the importance of complex biogeochemical processes that include carbon, sulfur and nitrogen driven by physical activity and chemical releases of FTW plant roots.

 

I chose this paper because I am interested in the role that microbes have in bioremediation of wastes. I found it interesting that the article focused on which microbes were surrounding the FTWs roots and how they could be contributing to denitrification and sulfur  oxidation or sulfide reduction. I thought it was equally interesting that the condition of the plants’ rhizospheres could determine what microbes were present. This article could have serious implications for further studies and for finding further ways to incorporate plants and microbes into bioremediation.

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Citation:

Falkowski, P., T. Fenchel, and E. Delong. 2008. The microbial engines that drive the earths biogeochemical cycles. Science. 302, 5879:1034-1039.

 

Full article: https://science.sciencemag.org/content/320/5879/1034.full

 

Abstract:

Virtually all nonequilibrium electron transfers on Earth are driven by a set of nanobiological machines composed largely of multimeric protein complexes associated with a small number of prosthetic groups. These machines evolved exclusively in microbes early in our planet’s history yet, despite their antiquity, are highly conserved. Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales.

 

I chose this article because of the great explanations of microbial involvement in biogeochemical cycling on a chemical basis, touches on the evolution of these processes, and explains how they control activity on different levels.

 

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Citation:

Ren, Z., Gao, H., Elser, J. J., & Zhao, Q. (2017). Microbial functional genes elucidate environmental drivers of biofilm metabolism in glacier-fed streams.  Scientific reports,  7(1), 12668.

https://www.nature.com/articles/s41598-017-13086-9.pdf

Abstract:

Benthic biofilms in glacier-fed streams harbor diverse microorganisms driving biogeochemical cycles and, consequently, influencing ecosystem-level processes. Benthic biofilms are vulnerable to glacial retreat induced by climate change. To investigate microbial functions of benthic biofilms in glacier-fed streams, we predicted metagenomes from 16s rRNA gene sequence data using PICRUSt and identified functional genes associated with nitrogen and sulfur metabolisms based on KEGG database and explored the relationships between metabolic pathways and abiotic factors in glacier-fed streams in the Tianshan Mountains in Central Asia. Results showed that the distribution of functional genes was mainly associated with glacier area proportion, glacier source proportion, total nitrogen, dissolved organic carbon, and pH. For nitrogen metabolism, the relative abundance of functional genes associated with dissimilatory pathways was higher than those for assimilatory pathways. The relative abundance of functional genes associated with assimilatory sulfate reduction was higher than those involved with the sulfur oxidation system and dissimilatory sulfate reduction. Hydrological factors had more significant correlations with nitrogen metabolism than physicochemical factors and anammox was the most sensitive nitrogen cycling pathway responding to variation of the abiotic environment in these glacial-fed streams. In contrast, sulfur metabolism pathways were not sensitive to variations of abiotic factors in these systems.

 

I chose this article because I am very interested in biogeochemical cycling within stream biofilms, and how the diversity of microorganisms present can influence ecosystem processes. Adding glaciers to the mix just makes it more exciting! This article also uses methods we have learned about in class  (16srRNA gene sequencing), so the paper helped me better understand how these methods can be used in another environmental application.

 

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“Bacterial biofilms on gold grains–implications for geomicrobial transformations of gold”

ABSTRACT

The biogeochemical cycling of gold (Au), i.e. its solubilization, transport and re-precipitation, leading to the (trans)formation of Au grains and nuggets has been demonstrated under a range of environmental conditions. Biogenic (trans)formations of Au grains are driven by (geo)biochemical processes mediated by distinct biofilm consortia living on these grains. This review summarizes the current knowledge concerning the composition and functional capabilities of Au-grain communities, and identifies contributions of key-species involved in Au-cycling. To date, community data are available from grains collected at 10 sites in Australia, New Zealand and South America. The majority of detected operational taxonomic units detected belong to the α-, β- and γ -Proteobacteria and the Actinobacteria. A range of organisms appears to contribute predominantly to biofilm establishment and nutrient cycling, some affect the mobilization of Au via excretion of Au-complexing ligands, e.g. organic acids, thiosulfate and cyanide, while a range of resident Proteobacteria, especially Cupriavidus metallidurans and Delftia acidovorans, have developed Au-specific biochemical responses to deal with Au-toxicity and reductively precipitate mobile Au-complexes. This leads to the biomineralization of secondary Au and drives the environmental cycle of Au.

 

CITATION

Rea, M. A., Zammit, C. M., & Reith, F. (2016, June 1). Bacterial biofilms on gold grains-implications for geomicrobial transformations of gold.  FEMS Microbiology Ecology. Oxford University Press. https://doi.org/10.1093/femsec/fiw082.

Link

 

JUSTIFICATION

Gold- a precious metal, revered since antiquity, mined on every continent (except Antartica)- is important to society. Previously, gold was thought to be biologically inactive but this is now known to be untrue. Discover more about what microbes can do with gold.

 

Abstract

Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and  Acidobacteria,  Protecobacteria, and  Actinobacteria  were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (P<0.05) at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05) correlation was existed between the soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (P<0.05) to the relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can’t directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.

Zhang, Yuguang et al. “An Integrated Study to Analyze Soil Microbial Community Structure and Metabolic Potential in Two Forest Types.’ Ed. A. Mark Ibekwe.  PLoS ONE  9.4 (2014): e93773.  PMC. Web. 8 Feb. 2018.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990527/

I picked this article because I’m interested in ecosystem processes, especially when they are related to the development of forests.

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Abstract

Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situ  colonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding’ with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection during  in situ  colonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition.

Stern, Noah et al. “Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor.’ Ed. Joel E. Kostka.  Applied and Environmental Microbiology  83.16 (2017): e00260—17.  PMC. Web. 8 Feb. 2018.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5541231/

 

This paper shows an intriguing concept on riverine microbial community composition and the effects that their biogeochemical cycling processes have on the freshwater environment.

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Abstract

The hyporheic zone (HZ) is the active ecotone between the surface stream and groundwater, where exchanges of nutrients and organic carbon have been shown to stimulate microbial activity and transformations of carbon and nitrogen. To examine the relationship between sediment texture, biogeochemistry, and biological activity in the Columbia River HZ, the grain size distributions for sediment samples were characterized to define geological facies, and the relationships among physical properties of the facies, physicochemical attributes of the local environment, and the structure and activity of associated microbial communities were examined. Mud and sand content and the presence of microbial heterotrophic and nitrifying communities partially explained the variability in many biogeochemical attributes such as C:N ratio and %TOC. Microbial community analysis revealed a high relative abundance of putative ammonia-oxidizing Thaumarchaeota and nitrite-oxidizing Nitrospirae. Network analysis showed negative relationships between sets of co-varying organisms and sand and mud contents, and positive relationships with total organic carbon. Our results indicate grain size distribution is a good predictor of biogeochemical properties, and that subsets of the overall microbial community respond to different sediment texture. Relationships between facies and hydrobiogeochemical properties enable facies-based conditional simulation/mapping of these properties to inform multiscale modeling of hyporheic exchange and biogeochemical processes.

Hou, Z. et al. “Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies.’  Scientific Reports  7 (2017): 12006.  PMC. Web. 8 Feb. 2018.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607297/

This paper presents an interesting perspective on how microbes can function in different types of sediments.

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